The technology disclosed extracts intensities from sequencing images for base calling target clusters and attenuates spatial crosstalk from neighboring clusters. The technology disclosed accesses a particular section from a plurality of sections of an image output by a sensor, the particular section of the image including at least one pixel depicting intensity emission values from a target cluster and neighboring clusters located across the sensor, and convolves the particular section of the image with a corresponding convolution kernel in a plurality of convolution kernels, to generate a feature map comprising a plurality of feature values. The technology disclosed further assigns a corresponding feature value to the target cluster based on feature values in the plurality of feature values adjoining a center of the target cluster, and processes the corresponding feature value assigned to the target cluster, to base call the target cluster.
Legal claims defining the scope of protection, as filed with the USPTO.
. A system comprising:
. The system of, further comprising computer instructions that, when executed by the one or more processors, cause the system to:
. The system of, further comprising instructions that, when executed by the one or more processors, cause the system to:
. The system of, wherein the location of target oligonucleotide cluster comprises a center of the target oligonucleotide cluster.
. The system of, further comprising computer instructions that, when executed by the one or more processors, cause the system to:
. The system of, wherein:
. The system of, wherein:
. The system of, further comprising instructions that, when executed by the one or more processors, cause the system to determine the substrate-section-specific coefficients for an imaging channel of a set of imaging channels.
. The system of, further comprising computer instructions that, when executed by the one or more processors, cause the system to:
. The system of, further comprising computer instructions that, when executed by the one or more processors, cause the system to:
. A non-transitory computer readable storage medium storing computer instructions that, when executed by one or more processors, cause a system to:
. The non-transitory computer readable storage medium of, further storing computer instructions that, when executed by the one or more processors, cause the system to:
. The non-transitory computer readable storage medium of, wherein the location of target oligonucleotide cluster comprises a center of the target oligonucleotide cluster.
. The non-transitory computer readable storage medium of, further storing computer instructions that, when executed by the one or more processors, cause the system to:
. The non-transitory computer readable storage medium of, wherein:
. A computer-implemented method comprising:
. The computer-implemented method of, further comprising:
. The computer-implemented method of, wherein determining the substrate-section-specific coefficients comprises determining the substrate-section-specific coefficients for an imaging channel of a set of imaging channels.
. The computer-implemented method of, wherein:
. The computer-implemented method of, wherein:
Complete technical specification and implementation details from the patent document.
This application is a continuation of U.S. Nonprovisional patent application Ser. No. 18/604,194, entitled “INTENSITY EXTRACTION FOR FEATURE VALUES IN BASE CALLING,” filed on Mar. 13, 2024, which is a continuation of U.S. Nonprovisional patent application Ser. No. 17/902,630, entitled “INTENSITY EXTRACTION AND SPATIAL CROSSTALK ATTENUATION FOR BASE CALLING,” filed on Sep. 2, 2022, which is a continuation of U.S. Nonprovisional patent application Ser. No. 17/511,483, entitled “INTENSITY EXTRACTION AND CROSSTALK ATTENUATION USING INTERPOLATION AND ADAPTATION FOR BASE CALLING,” filed on Oct. 26, 2021, which in turn claims the priority to or benefit of U.S. Provisional Patent Application No. 63/223,408, entitled “SPECIALIST SIGNAL PROFILERS FOR BASE CALLING,” filed on Jul. 19, 2021. Each of the aforementioned applications is hereby incorporated by reference in its entirety.
Pursuant to 35 USC § 102 (b)(2)(C) and MPEP § 2146.02 (I), Applicant hereby states that this application, U.S. Provisional Patent Application No. 63/020,449, and U.S. Nonprovisional patent application Ser. No. 17/308,035, not later than the effective filing date of this application, were owned by or subject to an obligation of assignment to the same person (Illumina, Inc.), and that Illumina Software, Inc., the named applicant and assignee on this application, is a wholly owned subsidiary of Illumina, Inc.
The technology disclosed relates to artificial intelligence type computers and digital data processing systems and corresponding data processing methods and products for emulation of intelligence (i.e., knowledge based systems, reasoning systems, and knowledge acquisition systems); and including systems for reasoning with uncertainty (e.g., fuzzy logic systems), adaptive systems, machine learning systems, and artificial neural networks. In particular, the technology disclosed relates to using deep neural networks such as deep convolutional neural networks for analyzing data.
The following are incorporated by reference for all purposes as if fully set forth herein:
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The subject matter discussed in this section should not be assumed to be prior art merely as a result of its mention in this section. Similarly, a problem mentioned in this section or associated with the subject matter provided as background should not be assumed to have been previously recognized in the prior art. The subject matter in this section merely represents different approaches, which in and of themselves can also correspond to implementations of the claimed technology.
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October 2, 2025
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